[gmx-users] rather theoretical question

[Dmitry Egorov]

Dear Gromacs users, could anybody answer next question.

Suppose, we have two different conformations of the same enzyme-cofactor complex,say, C1 and C2. Further, conformations of ligand binding sites and ligands themselves are also different for these C1 and C2 states. Then we place,say, ligand in conformation from C2 to binding site of C1 ( with previously deleted C1 ligand ). How is it reasonable  to wait that MD convert C2 ligand conformation to right for receptor C1 state and reproduce right ligand fit. What complications may occur here.

Thanks for your attention to my problem.
D. Egorov
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